Writing flexible document outputs with Markdown syntax

ANU BDSI
workshop Reproducible research with Quarto

Emi Tanaka

Biological Data Science Institute

12th April 2024

Welcome 👋

Teaching team

  • Academic statistician passionate about data science and open source software
  • Currently, Deputy Director of ANU Biological Data Science Institute and Executive Editor of R Journal
  • PhD in Statistical Bioinformatics
  • BSci (Adv Maths) with major in Mathematics and Statistics
  • Loves data and coding

        https://emitanaka.org     @statsgen     fosstodon.org/@emitanaka

  • 2nd year of PhD student at ANU, working on phylogenomics methods to study hybridisation
  • BSci in Bioinformatics
  • Enjoy hiking and science
  • jeremiasivan
  • (Almost finishing) PhD student @Moritz Lab, E&E Division, RSB, ANU
  • Working on historical biogeography of Indo-Australian birds
  • BSc (Hons) with major in Zoology and Ecology & Conservation
  • Loves games, art markets, and FOOD
  • @goaudreymp
  • https://linktr.ee/goaudreymp
  • 3rd Year PhD student @ Linde Lab, E&E Division, RSB, ANU
  • Investigating the evolution of the Australian orchid flora and associated funga
  • MScSt (Biodiversity Science)
  • Loves playing music, reading, nature
  • @rpodonnell
  • rpodonnell.github.io
  • 2nd Year PhD student @ Sequeira Lab, E&E Division, RSB, ANU
  • Identifying social, collective, or coordinated movement behaviour patterns in sharks using tracking data
  • MSc (Marine Biology), BSc (Biology)
  • Loves triathlon, hiking and the ocean
  • @nilskreuter
  • https://linktr.ee/nilskreuter

Workshop materials

All materials will be hosted at
https://anu-bdsi.github.io/workshop-intro-quarto/

Today’s learning objectives

  • Generate HTML, PDF, or Word documents using Markdown syntax
  • Understand the anatomy of Quarto documents
  • Develop dynamic documents containing code (in R, Python, or Julia) using Quarto
  • Implement various code chunk options to customize chunk behaviour
  • Recognize the significance of reproducibility and grasp the concept of literate programming
  • Apply reproducible practices
  • Establish an organized folder structure for data projects

Current learning objective

  • Generate HTML, PDF, or Word documents using Markdown syntax
  • Understand the anatomy of Quarto documents
  • -Develop dynamic documents containing code (in R, Python, or Julia) using Quarto
  • -Implement various code chunk options to customize chunk behaviour
  • -Recognize the significance of reproducibility and grasp the concept of literate programming
  • -Apply reproducible practices
  • -Establish an organized folder structure for data projects

anu-bdsi.github.io/workshop-intro-quarto/